Hello!
We formatted freshly recorded MEG & anatomical MRI data to BIDS and then used the mne-bids-pipeline (1.9), as well as manual co-registration using the gui.
Do I remember correctly that we need to update the anatomical landmarks in the BIDS dataset manually using mne_bids.get_anat_landmarks and mne_bids.update_anat_landmarks?
Is this documented somewhere? If not, I think we should add it.
Hi Sophie,
I don’t have time to look into this now in detail, but I believe you’re right. This was always a bit of a crux 
I’d love the re-imagine this entire workflow somehow; for example, what if doing the coregistration would update the BIDS data automatically? 
Richard
+1 for making the coregistration part of the pipeline (it currently is not). maybe with a config parameter that switches to an interactive mode to be able to use the gui. I will work on the code we use and see whether we can make a suggestion / PR.
I guess I was more thinking about something along the lines of mne-bids coregistration, but then realized that we first need to run FreeSurfer… so yes, maybe doing it via MNE-BIDS-Pipeline does make more sense.
I thought about adding it to the freesurfer-commands (05), right after creating coregistration surfaces. that makes it kind of more optional.